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New Phytol. 2018 Jun;218(4):1645-1657. doi: 10.1111/nph.15098. Epub 2018 Mar 25.

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

Yang X1,2, Zhao H1,3, Zhang T1,4, Zeng Z1,3, Zhang P1,5, Zhu B1, Han Y1,6, Braz GT1,7, Casler MD8, Schmutz J9,10, Jiang J1,3.

Author information

1
Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
2
Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
3
Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
4
Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
5
College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
6
School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
7
Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil.
8
Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI, 53706, USA.
9
Joint Genome Institute, Walnut Creek, CA, 94598, USA.
10
HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.

Abstract

Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat.

KEYWORDS:

cenH3 nucleosome; centromere; centromere evolution; satellite repeats; switchgrass (Panicum virgatum)

PMID:
29577299
DOI:
10.1111/nph.15098

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